In the last decades, there has been an increasing interest in gender differences with regard to achievement in different subject areas and at different levels of education, as well as with regard to attitudes towards science. Evidence based decision making in education and consideration of possible inequalities between genders are necessary for improvement of the quality of education for all students. Using the PISA 2006 database that enables investigation of the reading, mathematics and science achievement of Slovenian students at the beginning of upper-secondary education we will further investigate the profiles of female and male student achievement in these areas. In previous analyses (Straus, in press) it has been shown that findings about gender differences in the overall population of 15-year-olds change considerably when gender differences are studied within individual educational programs. Additional analyses will be carried out trying to reveal more detailed information on gender differences in Slovenia, for examples profiles of female and male students achieving at certain levels with regard to home and school background characteristics and others. Similarities with student profiles from some other countries will also be investigated.